LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -35.421485 0.0000000) to (16.697848 35.421485 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9111318 4.8617725 4.0498230 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -35.421485 0.0000000) to (16.697848 35.421485 4.0498230) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9111318 4.8617725 4.0498230 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -35.421485 0.0000000) to (16.697848 35.421485 4.0498230) create_atoms CPU = 0.001 seconds 206 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 26 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_856956178669_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.438 | 4.438 | 4.438 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1190.3612 0 -1190.3612 165685.64 82 0 -1741.3169 0 -1741.3169 7395.8355 Loop time of 1.47287 on 1 procs for 82 steps with 408 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1190.36116288269 -1741.31526490286 -1741.31693885685 Force two-norm initial, final = 1140.6980 0.15029683 Force max component initial, final = 380.45380 0.022316240 Final line search alpha, max atom move = 1.0000000 0.022316240 Iterations, force evaluations = 82 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4597 | 1.4597 | 1.4597 | 0.0 | 99.10 Neigh | 0.0062173 | 0.0062173 | 0.0062173 | 0.0 | 0.42 Comm | 0.0033932 | 0.0033932 | 0.0033932 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003579 | | | 0.24 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2321.00 ave 2321 max 2321 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23844.0 ave 23844 max 23844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23844 Ave neighs/atom = 58.441176 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.438 | 4.438 | 4.438 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -1741.3169 0 -1741.3169 7395.8355 4790.6376 87 0 -1741.4154 0 -1741.4154 267.66457 4809.4988 Loop time of 0.0791657 on 1 procs for 5 steps with 408 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1741.31693885685 -1741.41475119054 -1741.41544753575 Force two-norm initial, final = 46.640010 1.5528468 Force max component initial, final = 41.735604 1.1388785 Final line search alpha, max atom move = 0.00032175196 0.00036643638 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.078284 | 0.078284 | 0.078284 | 0.0 | 98.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014435 | 0.00014435 | 0.00014435 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000737 | | | 0.93 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2329.00 ave 2329 max 2329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23808.0 ave 23808 max 23808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23808 Ave neighs/atom = 58.352941 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1741.4154 0 -1741.4154 267.66457 Loop time of 2.023e-06 on 1 procs for 0 steps with 408 atoms 148.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.023e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2329.00 ave 2329 max 2329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23808.0 ave 23808 max 23808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23808 Ave neighs/atom = 58.352941 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.576 | 4.576 | 4.576 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -1741.4154 -1741.4154 16.719193 71.13554 4.0438764 267.66457 267.66457 323.47417 380.95861 98.56094 2.2884387 278.67312 Loop time of 1.888e-06 on 1 procs for 0 steps with 408 atoms 211.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.888e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2329.00 ave 2329 max 2329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11904.0 ave 11904 max 11904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23808.0 ave 23808 max 23808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23808 Ave neighs/atom = 58.352941 Neighbor list builds = 0 Dangerous builds = 0 408 -1741.41544753575 eV 2.28843868856029 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01